Alternative splicing and evolution: diversification, exon definition and function

Initial sequencing and analysis of the human genome

International Human Genome Sequencing Consortium, Whitehead Institute for Biomedical Research, C. F. G. R., Lander, E. S., Linton, L. M., Birren, B., Nusbaum, C., Zody, M. C., Baldwin, J., Devon, K., Dewar, K., et al. (2001) · Nature · doi:10.1038/35057062 · Cited by 24,216 · see citing works

Alternative isoform regulation in human tissue transcriptomes

Wang, E. T., Sandberg, R., Luo, S., Khrebtukova, I., Zhang, L., Mayr, C., Kingsmore, S. F., Schroth, G. P., & Burge, C. B. (2008) · Nature · doi:10.1038/nature07509 · Cited by 5,181 · see citing works

Mechanisms of Alternative Pre-Messenger RNA Splicing

Black, D. L. (2003) · Annual Review of Biochemistry · doi:10.1146/annurev.biochem.72.121801.161720 · Cited by 2,704 · see citing works

Why genes in pieces?

Gilbert, W. (1978) · Nature · doi:10.1038/271501a0 · Cited by 2,300 · see citing works

Listening to silence and understanding nonsense: exonic mutations that affect splicing

Cartegni, L., Chew, S. L., & Krainer, A. R. (2002) · Nature Reviews Genetics · doi:10.1038/nrg775 · Cited by 2,209 · see citing works

A genomic view of alternative splicing

Modrek, B., & Lee, C. (2002) · Nature Genetics · doi:10.1038/ng0102-13 · Cited by 1,307 · see citing works

Mechanisms of alternative splicing regulation: insights from molecular and genomics approaches

Chen, M., & Manley, J. L. (2009) · Nature Reviews Molecular Cell Biology · doi:10.1038/nrm2777 · Cited by 1,284 · see citing works

RNA Editing by Adenosine Deaminases That Act on RNA

Bass, B. (2002) · Annual Review of Biochemistry · doi:10.1146/annurev.biochem.71.110601.135501 · Cited by 1,272 · see citing works

Drosophila Dscam Is an Axon Guidance Receptor Exhibiting Extraordinary Molecular Diversity

Schmucker, D., Clemens, J. C., Shu, H., Worby, C. A., Xiao, J. Y., Muda, M., Dixon, J. E., & Zipursky, S. L. (2000) · Cell · doi:10.1016/s0092-8674(00)80878-8 · Cited by 1,105 · see citing works

Regulation of Alternative Splicing by Histone Modifications

Luco, R. F., Pan, Q., Tominaga, K., Blencowe, B. J., Pereira‐Smith, O. M., & Misteli, T. (2010) · Science · doi:10.1126/science.1184208 · Cited by 1,099 · see citing works

Splicing regulation: From a parts list of regulatory elements to an integrated splicing code

Wang, Z., & Burge, C. B. (2008) · RNA · doi:10.1261/rna.876308 · Cited by 1,076 · see citing works

Splicing in disease: disruption of the splicing code and the decoding machinery

Wang, G., & Cooper, T. A. (2007) · Nature Reviews Genetics · doi:10.1038/nrg2164 · Cited by 1,040 · see citing works

RNA processing and its regulation: global insights into biological networks

Licatalosi, D. D., & Darnell, R. B. (2009) · Nature Reviews Genetics · doi:10.1038/nrg2673 · Cited by 760 · see citing works

Widespread A-to-I RNA Editing of Alu-Containing mRNAs in the Human Transcriptome

Athanasiadis, A., Rich, A. S., & Maas, S. (2004) · PLoS Biology · doi:10.1371/journal.pbio.0020391 · Cited by 743 · see citing works

Differential chromatin marking of introns and expressed exons by H3K36me3

Kolasinska-Zwierz, P., Down, T. A., Latorre, I. J., Liu, T., Liu, X. S., & Ahringer, J. (2009) · Nature Genetics · doi:10.1038/ng.322 · Cited by 671 · see citing works

Chromatin organization marks exon-intron structure

Schwartz, S., Meshorer, E., & Ast, G. (2009) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1659 · Cited by 638 · see citing works

Aberrant and Alternative Splicing in Cancer

Venables, J. P. (2004) · Cancer Research · doi:10.1158/0008-5472.can-04-1910 · Cited by 630 · see citing works

How did alternative splicing evolve?

Ast, G. (2004) · Nature Reviews Genetics · doi:10.1038/nrg1451 · Cited by 544 · see citing works

Alternative splicing and disease

Tazi, J., Bakkour, N., & Stamm, S. (2008) · Biochimica et Biophysica Acta (BBA) - Molecular Basis of Disease · doi:10.1016/j.bbadis.2008.09.017 · Cited by 541 · see citing works

The multiplicity of domains in proteins.

Doolittle, R. (1995) · Annual Review of Biochemistry · doi:10.1146/annurev.bi.64.070195.001443 · Cited by 540 · see citing works

Alternative splicing in disease and therapy

Garcia-Blanco, M. A., Baraniak, A. P., & Lasda, E. L. (2004) · Nature Biotechnology · doi:10.1038/nbt964 · Cited by 527 · see citing works

Alternative splicing in the human, mouse and rat genomes is associated with an increased frequency of exon creation and/or loss

Modrek, B., & Lee, C. J. (2003) · Nature Genetics · doi:10.1038/ng1159 · Cited by 523 · see citing works

Alu -Containing Exons are Alternatively SplicedPreprint

Sorek, R., Ast, G., & Graur, D. (2002) · Genome Research · doi:10.1101/gr.229302 · Cited by 507 · see citing works

Nucleosome positioning as a determinant of exon recognition

Tilgner, H., Nikolaou, C., Althammer, S., Sammeth, M., Beato, M., Valcárcel, J., & Guigó, R. (2009) · Nature Structural & Molecular Biology · doi:10.1038/nsmb.1658 · Cited by 446 · see citing works

Remarkable Interkingdom Conservation of Intron Positions and Massive, Lineage-Specific Intron Loss and Gain in Eukaryotic Evolution

Rogozin, I. B., Wolf, Y. I., Sorokin, A. V., Mirkin, B. G., & Koonin, E. V. (2003) · Current Biology · doi:10.1016/s0960-9822(03)00558-x · Cited by 445 · see citing works

The Birth of an Alternatively Spliced Exon: 3' Splice-Site Selection in Alu Exons

Lev-Maor, G., Sorek, R., Shomron, N., & Ast, G. (2003) · Science · doi:10.1126/science.1082588 · Cited by 435 · see citing works

Transposable elements are found in a large number of human protein-coding genes

Nekrutenko, A., & Li, W.-H. (2001) · Trends in Genetics · doi:10.1016/s0168-9525(01)02445-3 · Cited by 430 · see citing works

Genome evolution and the evolution of exon-shuffling — a review

Patthy, L. (1999) · Gene · doi:10.1016/s0378-1119(99)00228-0 · Cited by 423 · see citing works

Nucleosomal Fluctuations Govern the Transcription Dynamics of RNA Polymerase II

Hodges, H. C., Bintu, L., Lubkowska, L., Kashlev, M., & Bustamante, C. (2009) · Science · doi:10.1126/science.1172926 · Cited by 368 · see citing works

Nucleosomes are well positioned in exons and carry characteristic histone modifications

Andersson, R., Enroth, S., Rada-Iglesias, A., Wadelius, C., & Komorowski, J. (2009) · Genome Research · doi:10.1101/gr.092353.109 · Cited by 325 · see citing works

How prevalent is functional alternative splicing in the human genome?

Sorek, R., Shamir, R., & Ast, G. (2003) · Trends in Genetics · doi:10.1016/j.tig.2003.12.004 · Cited by 305 · see citing works

Intron phase correlations and the evolution of the intron/exon structure of genes.

Long, M., Rosenberg, C., & Gilbert, W. (1995) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.92.26.12495 · Cited by 302 · see citing works

Intron‐dependent evolution: Preferred types of exons and introns

Patthy, L. (1987) · FEBS Letters · doi:10.1016/0014-5793(87)80002-9 · Cited by 300 · see citing works

Identification and analysis of alternative splicing events conserved in human and mouse

Yeo, G. W.-M., Nostrand, E. L. V., Holste, D., Poggio, T., & Burge, C. B. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0409742102 · Cited by 299 · see citing works

Alu sequences in the coding regions of mRNA: a source of protein variability

Makałowski, W., Mitchell, G. A., & Labuda, D. (1994) · Trends in Genetics · doi:10.1016/0168-9525(94)90254-2 · Cited by 286 · see citing works

Directed evolution of proteins by exon shuffling

Kolkman, J. A., & Stemmer, W. P. C. (2001) · Nature Biotechnology · doi:10.1038/88084 · Cited by 274 · see citing works

The architecture of pre-mRNAs affects mechanisms of splice-site pairing

Fox-Walsh, K. L., Dou, Y., Lam, B. J., Hung, S., Baldi, P., & Hertel, K. J. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0508489102 · Cited by 267 · see citing works

Alternative splicing and RNA selection pressure — evolutionary consequences for eukaryotic genomes

Xing, Y., & Lee, C. J. (2006) · Nature Reviews Genetics · doi:10.1038/nrg1896 · Cited by 259 · see citing works

Origin of Primate Orphan Genes: A Comparative Genomics Approach

Toll‐Riera, M., van den Bosch, N., Bellora, N., Castelo, R., Armengol, L., Estivill, X., & Albà, M. M. (2008) · Molecular Biology and Evolution · doi:10.1093/molbev/msn281 · Cited by 241 · see citing works

Comparative analysis of transposed element insertion within human and mouse genomes reveals Alu's unique role in shaping the human transcriptome

Sela, N., Mersch, B., Gal-Mark, N., Lev-Maor, G., Hotz‐Wagenblatt, A., & Ast, G. (2007) · Genome biology · doi:10.1186/gb-2007-8-6-r127 · Cited by 233 · see citing works

Translational control of intron splicing in eukaryotes

Jaillon, O., Bouhouche, K., Goût, J.-F., Aury, J., Noël, B., Saudemont, B., Nowacki, M., Serrano, V., Porcel, B. M., Segurens, B., et al. (2008) · Nature · doi:10.1038/nature06495 · Cited by 224 · see citing works

TRANSCRIPTOME AND GENOME CONSERVATION OF ALTERNATIVE SPLICING EVENTS IN HUMANS AND MICE

Sugnet, C. W., Kent, W. J., Ares, M., & Haussler, D. H. (2003) · Pacific Symposium on Biocomputing (PSB) · doi:10.1142/9789812704856_0007 · Cited by 222 · see citing works

Alternative splicing: current perspectives

Kim, E., Goren, A., & Ast, G. (2007) · BioEssays · doi:10.1002/bies.20692 · Cited by 218 · see citing works

Rates of intron loss and gain: Implications for early eukaryotic evolution

Roy, S. W., & Gilbert, W. (2005) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.0500383102 · Cited by 214 · see citing works

RNA-editing-mediated exon evolution

Lev-Maor, G., Sorek, R., Levanon, E. Y., Paz-Yaacov, N., Eisenberg, E., & Ast, G. (2007) · Genome biology · doi:10.1186/gb-2007-8-2-r29 · Cited by 203 · see citing works

The birth of new exons: Mechanisms and evolutionary consequences

Sorek, R. (2007) · RNA · doi:10.1261/rna.682507 · Cited by 193 · see citing works

Large-scale comparison of intron positions among animal, plant, and fungal genes

Fedorov, A. N., Merican, A. F., & Gilbert, W. (2002) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.242624899 · Cited by 189 · see citing works

Stochastic noise in splicing machinery

Melamud, E., & Moult, J. (2009) · Nucleic Acids Research · doi:10.1093/nar/gkp471 · Cited by 188 · see citing works

Large-scale comparative analysis of splicing signals and their corresponding splicing factors in eukaryotesPreprint

Schwartz, S., Silva, J., Burstein, D., Pupko, T., Eyras, E., & Ast, G. (2007) · Genome Research · doi:10.1101/gr.6818908 · Cited by 186 · see citing works

Architectural limits on split genes

Sterner, D. A., Carlo, T., & Berget, S. M. (1996) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.93.26.15081 · Cited by 185 · see citing works

Three distinct modes of intron dynamics in the evolution of eukaryotesPreprint

Carmel, L., Wolf, Y. I., Rogozin, I. B., & Koonin, E. V. (2007) · Genome Research · doi:10.1101/gr.6438607 · Cited by 178 · see citing works

Minimal Conditions for Exonization of Intronic Sequences

Sorek, R., Lev-Maor, G., Reznik, M., Dagan, T., Belinky, F., Graur, D., & Ast, G. (2004) · Molecular Cell · doi:10.1016/s1097-2765(04)00181-9 · Cited by 169 · see citing works

Intronic Alus Influence Alternative Splicing

Lev-Maor, G., Ram, O., Kim, E., Sela, N., Goren, A., Levanon, E. Y., & Ast, G. (2008) · PLoS Genetics · doi:10.1371/journal.pgen.1000204 · Cited by 169 · see citing works

Inter‐kingdom conservation of mechanism of nonsense‐mediated mRNA decay

Kerényi, Z., Mérai, Z., Hiripi, L., Benkovics, A. H., Gyula, P., Lacomme, C., Barta, E., Nagy, F., & Silhavy, D. (2008) · The EMBO Journal · doi:10.1038/emboj.2008.88 · Cited by 168 · see citing works

Sequence features responsible for intron retention in human

Sakabe, N. J., & de Souza, S. (2007) · BMC Genomics · doi:10.1186/1471-2164-8-59 · Cited by 164 · see citing works

Common exon duplication in animals and its role in alternative splicing

Letunić, I. (2002) · Human Molecular Genetics · doi:10.1093/hmg/11.13.1561 · Cited by 163 · see citing works

Origin of alternative splicing by tandem exon duplication

Kondrashov, F. A. (2001) · Human Molecular Genetics · doi:10.1093/hmg/10.23.2661 · Cited by 154 · see citing works

Current topics in genome evolution: Molecular mechanisms of new gene formation

Babushok, D. V., Ostertag, E. M., & Kazazian, H. H. (2006) · Cellular and Molecular Life Sciences · doi:10.1007/s00018-006-6453-4 · Cited by 149 · see citing works

Alternative splicing of conserved exons is frequently species-specific in human and mouse

Pan, Q., Bakowski, M. A., Morris, Q., Zhang, W., Frey, B. J., Hughes, T. R., & Blencowe, B. J. (2004) · Trends in Genetics · doi:10.1016/j.tig.2004.12.004 · Cited by 149 · see citing works

Low conservation of alternative splicing patterns in the human and mouse genomes

Nurtdinov, R. (2003) · Human Molecular Genetics · doi:10.1093/hmg/ddg137 · Cited by 147 · see citing works

Barriers to Intron Promiscuity in Bacteria

Edgell, D. R., Belfort, M., & Shub, D. A. (2000) · Journal of Bacteriology · doi:10.1128/jb.182.19.5281-5289.2000 · Cited by 146 · see citing works

RNA editing: a driving force for adaptive evolution?

Gommans, W. M., Mullen, S. P., & Maas, S. (2009) · BioEssays · doi:10.1002/bies.200900045 · Cited by 146 · see citing works

Alu-SINE Exonization: En Route to Protein-Coding Function

Krull, M., Brosius, J., & Schmitz, J. (2005) · Molecular Biology and Evolution · doi:10.1093/molbev/msi164 · Cited by 142 · see citing works

Protein domains correlate strongly with exons in multiple eukaryotic genomes – evidence of exon shuffling?

Liu, M., & Grigoriev, A. (2004) · Trends in Genetics · doi:10.1016/j.tig.2004.06.013 · Cited by 136 · see citing works

Global analysis of exon creation versus loss and the role of alternative splicing in 17 vertebrate genomes

Alekseyenko, A. V., Kim, N., & Lee, C. J. (2007) · RNA · doi:10.1261/rna.325107 · Cited by 134 · see citing works

Conservation of human alternative splice events in mouse

Thanaraj, T. A. (2003) · Nucleic Acids Research · doi:10.1093/nar/gkg355 · Cited by 133 · see citing works

Exaptation of an ancient Alu short interspersed element provides a highly conserved vitamin D-mediated innate immune response in humans and primates

Gombart, A. F., Saito, T., & Koeffler, H. P. (2009) · BMC Genomics · doi:10.1186/1471-2164-10-321 · Cited by 131 · see citing works

Short interspersed elements (SINEs) are a major source of canine genomic diversityPreprint

Wang, W., & Kirkness, E. F. (2005) · Genome Research · doi:10.1101/gr.3765505 · Cited by 125 · see citing works

Extensive, Recent Intron Gains in Daphnia Populations

Li, W., Tucker, A. E., Sung, W., Thomas, W. K., & Lynch, M. (2009) · Science · doi:10.1126/science.1179302 · Cited by 122 · see citing works

Diverse Splicing Patterns of Exonized Alu Elements in Human Tissues

Lin, L., Shen, S., Tye, A., Cai, J. J., Jiang, P., Davidson, B. L., & Xing, Y. (2008) · PLoS Genetics · doi:10.1371/journal.pgen.1000225 · Cited by 116 · see citing works

Nucleosomes are preferentially positioned at exons in somatic and sperm cells

Nahkuri, S., Taft, R. J., & Mattick, J. S. (2009) · Cell Cycle · doi:10.4161/cc.8.20.9916 · Cited by 106 · see citing works

Evolution of alternative splicing: deletions, insertions and origin of functional parts of proteins from intron sequences

Kondrashov, F. A., & Koonin, E. V. (2003) · Trends in Genetics · doi:10.1016/s0168-9525(02)00029-x · Cited by 106 · see citing works

Origin and evolution of new exons in rodentsPreprint

Wang, W., Zheng, H., Yang, S., et al. (2005) · Genome Research · doi:10.1101/gr.3929705 · Cited by 106 · see citing works

Exon shuffling and other ways of module exchange

Patthy, L. (1996) · Matrix Biology · doi:10.1016/s0945-053x(96)90131-6 · Cited by 105 · see citing works

Systematic genome-wide annotation of spliceosomal proteins reveals differential gene family expansionPreprint

Barbosa‐Morais, N. L., Carmo‐Fonseca, M., & Aparicio, S. A. J. R. (2005) · Genome Research · doi:10.1101/gr.3936206 · Cited by 98 · see citing works

Modulating the Expression of Disease Genes with RNA-Based Therapy

Wood, M. J. A., Yin, H., & McClorey, G. (2007) · PLoS Genetics · doi:10.1371/journal.pgen.0030109 · Cited by 98 · see citing works

Evolution of the sugar receptors in insects

Kent, L. B., & Robertson, H. M. (2009) · BMC Evolutionary Biology · doi:10.1186/1471-2148-9-41 · Cited by 94 · see citing works

The origins and implications of Aluternative splicing

Kreahling, J. M. (2003) · Trends in Genetics · doi:10.1016/j.tig.2003.11.001 · Cited by 94 · see citing works

The Emergence of Alternative 3′ and 5′ Splice Site Exons from Constitutive Exons

Koren, E., Lev-Maor, G., & Ast, G. (2007) · PLoS Computational Biology · doi:10.1371/journal.pcbi.0030095 · Cited by 87 · see citing works

Functional and evolutionary analysis of alternatively spliced genes is consistent with an early eukaryotic origin of alternative splicing

Irimia, M., Rukov, J. L., Penny, D., & Roy, S. W. (2007) · BMC Evolutionary Biology · doi:10.1186/1471-2148-7-188 · Cited by 87 · see citing works

New Maximum Likelihood Estimators for Eukaryotic Intron Evolution

Nguyen, H. D., Yoshihama, M., & Kenmochi, N. (2005) · PLoS Computational Biology · doi:10.1371/journal.pcbi.0010079 · Cited by 82 · see citing works

Patterns of intron gain and conservation in eukaryotic genes

Carmel, L., Rogozin, I. B., Wolf, Y. I., & Koonin, E. V. (2007) · BMC Evolutionary Biology · doi:10.1186/1471-2148-7-192 · Cited by 80 · see citing works

From “Junk” to Gene: Curriculum vitae of a Primate Receptor Isoform Gene

Singer, S. S., Männel, D. N., Hehlgans, T., et al. (2004) · Journal of Molecular Biology · doi:10.1016/j.jmb.2004.06.070 · Cited by 73 · see citing works

Structural organization of the 5′ region of the thyroglobulin gene

Parma, J., Christophe, D., Pohl, V., et al. (1987) · Journal of Molecular Biology · doi:10.1016/0022-2836(87)90403-7 · Cited by 71 · see citing works

Introns in protein‐coding genes in Archaea

Watanabe, Y., Yokobori, S., Inaba, T., et al. (2001) · FEBS Letters · doi:10.1016/s0014-5793(01)03219-7 · Cited by 69 · see citing works

Decrypting the genome's alternative messages

Hartmann, B., & Valcárcel, J. (2009) · Current Opinion in Cell Biology · doi:10.1016/j.ceb.2009.02.006 · Cited by 67 · see citing works

The “Alternative” Choice of Constitutive Exons throughout Evolution

Lev-Maor, G., Goren, A., Sela, N., et al. (2007) · PLoS Genetics · doi:10.1371/journal.pgen.0030203 · Cited by 66 · see citing works

Alu Exonization Events Reveal Features Required for Precise Recognition of Exons by the Splicing Machinery

Schwartz, S., Gal-Mark, N., Kfir, N., Ram, O., Kim, E., & Ast, G. (2009) · PLoS Computational Biology · doi:10.1371/journal.pcbi.1000300 · Cited by 65 · see citing works

Widespread Evolutionary Conservation of Alternatively Spliced Exons in Caenorhabditis

Irimia, M., Rukov, J. L., Penny, D., García‐Fernàndez, J., Vinther, J., & Roy, S. W. (2007) · Molecular Biology and Evolution · doi:10.1093/molbev/msm262 · Cited by 65 · see citing works

The importance of being divisible by three in alternative splicing

Magen, A. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki858 · Cited by 65 · see citing works

Nucleosome dynamics IV. protein and DNA contributions in the chiral transition of the tetrasome, the histone (H3-H4)2 tetramer-DNA particle

Alilat, M., Sivolob, A., Révet, B., et al. (1999) · Journal of Molecular Biology · doi:10.1006/jmbi.1999.2988 · Cited by 62 · see citing works

Chromatin Polymorphism and the Nucleosome Superfamily: A Genealogy

Lavelle, C., & Prunell, A. (2007) · Cell Cycle · doi:10.4161/cc.6.17.4631 · Cited by 59 · see citing works

Comparative Genomics and Evolution of Alternative Splicing: The Pessimists' Science

Artamonova, I. I., & Gelfand, M. S. (2007) · Chemical Reviews · doi:10.1021/cr068304c · Cited by 57 · see citing works

Nonsense-Mediated Decay Enables Intron Gain in Drosophila

Farlow, A., Meduri, E., Dolezal, M., Hua, L., & Schlötterer, C. (2010) · PLoS Genetics · doi:10.1371/journal.pgen.1000819 · Cited by 54 · see citing works

Extremely Intron-Rich Genes in the Alveolate Ancestors Inferred with a Flexible Maximum-Likelihood Approach

Csürös, M., Rogozin, I. B., & Koonin, E. V. (2008) · Molecular Biology and Evolution · doi:10.1093/molbev/msn039 · Cited by 53 · see citing works

Alternative splicing of Alu exons—two arms are better than one

Gal-Mark, N., Schwartz, S., & Ast, G. (2008) · Nucleic Acids Research · doi:10.1093/nar/gkn024 · Cited by 53 · see citing works

Positive selection acting on splicing motifs reflects compensatory evolutionPreprint

Ke, S., Zhang, X. H.-F., & Chasin, L. A. (2008) · Genome Research · doi:10.1101/gr.070268.107 · Cited by 52 · see citing works

Splicing in the eukaryotic ancestor: form, function and dysfunction

Roy, S. W., & Irimia, M. (2009) · Trends in Ecology & Evolution · doi:10.1016/j.tree.2009.04.005 · Cited by 52 · see citing works

SR proteins: a foot on the exon before the transition from intron to exon definition

Ram, O., & Ast, G. (2006) · Trends in Genetics · doi:10.1016/j.tig.2006.10.002 · Cited by 48 · see citing works

Beyond DNA: RNA Editing and Steps Toward Alu Exonization in Primates

Möller-Krull, M., Zemann, A., Roos, C., et al. (2008) · Journal of Molecular Biology · doi:10.1016/j.jmb.2008.07.014 · Cited by 48 · see citing works

Co-evolution of the branch site and SR proteins in eukaryotes

Plass, M., Agirre, E., Reyes-Garau, D., et al. (2008) · Trends in Genetics · doi:10.1016/j.tig.2008.10.004 · Cited by 45 · see citing works

Molecular mechanisms of exon shuffling: illegitimate recombination

van Rijk, A., & BLOEMENDAL, H. (2003) · Contemporary issues in genetics and evolution · doi:10.1007/978-94-010-0229-5_13 · Cited by 45 · see citing works

Large introns in relation to alternative splicing and gene evolution: a case study of Drosophila bruno-3

Kandul, N. P., & Noor, M. A. F. (2009) · BMC Genetics · doi:10.1186/1471-2156-10-67 · Cited by 44 · see citing works

Fast rate of evolution in alternatively spliced coding regions of mammalian genes

Ermakova, E. O., Nurtdinov, R., & Gelfand, M. S. (2006) · BMC Genomics · doi:10.1186/1471-2164-7-84 · Cited by 39 · see citing works

Exon creation and establishment in human genes

Corvelo, A., & Eyras, E. (2008) · Genome biology · doi:10.1186/gb-2008-9-9-r141 · Cited by 37 · see citing works

The Pivotal Roles of TIA Proteins in 5′ Splice-Site Selection of Alu Exons and Across Evolution

Gal-Mark, N., Schwartz, S., Ram, O., Eyras, E., & Ast, G. (2009) · PLoS Genetics · doi:10.1371/journal.pgen.1000717 · Cited by 36 · see citing works

Alternative splicing of anciently exonized 5S rRNA regulates plant transcription factor TFIIIAPreprint

Fu, Y., Bannach, O., Chen, H., et al. (2009) · Genome Research · doi:10.1101/gr.086876.108 · Cited by 36 · see citing works

Multifactorial Interplay Controls the Splicing Profile of Alu-Derived Exons

Ram, O., Schwartz, S., & Ast, G. (2008) · Molecular and Cellular Biology · doi:10.1128/mcb.02279-07 · Cited by 35 · see citing works

SERpredict: Detection of tissue- or tumor-specific isoforms generated through exonization of transposable elements

Mersch, B., Sela, N., Ast, G., et al. (2007) · BMC Genetics · doi:10.1186/1471-2156-8-78 · Cited by 35 · see citing works

Exonization of Alu-generated Splice Variants in the Survivin Gene of Human and Non-human Primates

Mola, G., Vela, E., Fernández‐Figueras, M. T., Isamat, M., & Muñoz-Mármol, A. M. (2006) · Journal of Molecular Biology · doi:10.1016/j.jmb.2006.11.089 · Cited by 34 · see citing works

Molecular Mechanisms of Exon Shuffling: Illegitimate Recombination

van Rijk, A., & Bloemendal, H. (2003) · Genetica · doi:10.1023/a:1024138600624 · Cited by 33 · see citing works

Differentiated evolutionary rates in alternative exons and the implications for splicing regulation

Plass, M., & Eyras, E. (2006) · BMC Evolutionary Biology · doi:10.1186/1471-2148-6-50 · Cited by 32 · see citing works

Tandem repeats modify the structure of human genes hosted in segmental duplications

Grassi, A., & Ciccarelli, F. D. (2009) · Genome biology · doi:10.1186/gb-2009-10-12-r137 · Cited by 32 · see citing works

Nucleosome conformational flexibility and implications for chromatin dynamics

Sivolob, A., & Prunell, A. (2004) · Philosophical Transactions of the Royal Society A Mathematical Physical and Engineering Sciences · doi:10.1098/rsta.2004.1387 · Cited by 30 · see citing works

Gain and loss of an intron in a protein-coding gene in Archaea: the case of an archaeal RNA pseudouridine synthase gene

Yokobori, S., Itoh, T., Yoshinari, S., et al. (2009) · BMC Evolutionary Biology · doi:10.1186/1471-2148-9-198 · Cited by 30 · see citing works

Extensive Exon Reshuffling Over Evolutionary Time Coupled to Trans -Splicing in DrosophilaPreprint

Labrador, M., & Corces, V. G. (2003) · Genome Research · doi:10.1101/gr.1440703 · Cited by 29 · see citing works

Exon shuffling mimicked in cell culture

van Rijk, A., JONG, W. W. D., & BLOEMENDAL, H. (1999) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.96.14.8074 · Cited by 28 · see citing works

An Alu insertion in compound heterozygosity with a microduplication in GNPTAB gene underlies Mucolipidosis II

Tappino, B., Regis, S., Corsolini, F., et al. (2007) · Molecular Genetics and Metabolism · doi:10.1016/j.ymgme.2007.09.010 · Cited by 23 · see citing works

Regulation of mammalian pre-mRNA splicing

Hui, J. (2009) · Science in China Series C Life Sciences · doi:10.1007/s11427-009-0037-0 · Cited by 23 · see citing works

Biased exonization of transposed elements in duplicated genes: A lesson from the TIF-IA gene

Amit, M., Sela, N., Keren, H., et al. (2007) · BMC Molecular Biology · doi:10.1186/1471-2199-8-109 · Cited by 23 · see citing works

Lineage specific evolutionary events on SFTPB gene: Alu recombination-mediated deletion (ARMD), exonization, and alternative splicing events

Lee, J.-R., Huh, J., Kim, D., et al. (2009) · Gene · doi:10.1016/j.gene.2009.01.008 · Cited by 13 · see citing works

Tandem exon duplication tends to propagate rather than to create de novo alternative splicing

Peng, T., & Li, Y. (2009) · Biochemical and Biophysical Research Communications · doi:10.1016/j.bbrc.2009.03.162 · Cited by 10 · see citing works

Revealing the hidden relationship between nucleosomes and splicing

Kaplan, C. D. (2009) · Cell Cycle · doi:10.4161/cc.8.22.10289 · Cited by 6 · see citing works

rMATS: robust and flexible detection of differential alternative splicing from replicate RNA-Seq data

Shen, S., Park, J. W., Lu, Z.-X., Lin, L., Henry, M. D., Wu, Y. N., Zhou, Q., & Xing, Y. (2014) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1419161111 · Cited by 2,713 · see citing works

Divergence of duplicate genes in exon-intron structure

Xu, G., Guo, C., Shan, H., & Kong, H. (2012) · Proceedings of the National Academy of Sciences · doi:10.1073/pnas.1109047109 · Cited by 1,072 · see citing works

The Evolutionary Landscape of Alternative Splicing in Vertebrate Species

Barbosa-Morais, N. L., Irimia, M., Pan, Q., Xiong, H. Y., Gueroussov, S., Lee, L. J., Slobodeniuc, V., Kutter, C., Watt, S., Çolak, R., et al. (2012) · Science · doi:10.1126/science.1230612 · Cited by 1,063 · see citing works

Context-dependent control of alternative splicing by RNA-binding proteins

Fu, X.-D., & Ares, M. (2014) · Nature Reviews Genetics · doi:10.1038/nrg3778 · Cited by 1,044 · see citing works

Function of alternative splicing

Kelemen, O., Convertini, P., Zhang, Z., Wen, Y., Shen, M., Falaleeva, M., & Stamm, S. (2013) · Gene · doi:10.1016/j.gene.2012.07.083 · Cited by 743 · see citing works

Tissue-specific splicing of disordered segments that embed binding motifs rewires protein interaction networks

Buljan, M., Chalancon, G., Eustermann, S., Wagner, G. P., Fuxreiter, M., Bateman, A., & Babu, M. M. (2012) · Molecular Cell · doi:10.1016/j.molcel.2012.05.039 · Cited by 396 · see citing works

Mechanisms and Regulation of Cellular Senescence

Roger, L., Tomas, F., & Gire, V. (2021) · International Journal of Molecular Sciences · doi:10.3390/ijms222313173 · Cited by 395 · see citing works

Differential GC content between exons and introns establishes distinct strategies of splice-site recognition

Amit, M., Donyo, M., Hollander, D., Goren, A., Kim, E., Gelfman, S., Lev-Maor, G., Burstein, D., Schwartz, S., Postolsky, B., et al. (2012) · Cell Reports · doi:10.1016/j.celrep.2012.03.013 · Cited by 338 · see citing works

Zebrafish mRNA sequencing deciphers novelties in transcriptome dynamics during maternal to zygotic transition

Aanes, H., Winata, C. L., Lin, C. H., Chen, J. P., Srinivasan, K. G., Lee, S. G. P., Lim, A. Y. M., Hajan, H. S., Collas, P., Bourque, G., et al. (2011) · Genome Research · doi:10.1101/gr.116012.110 · Cited by 285 · see citing works

Genetic Changes Shaping the Human Brain

Bae, B.-I., Jayaraman, D., & Walsh, C. A. (2015) · Developmental Cell · doi:10.1016/j.devcel.2015.01.035 · Cited by 135 · see citing works

Alternative pre-mRNA splicing in neurons: growing up and extending its reach

Zheng, S., & Black, D. L. (2013) · Trends in Genetics · doi:10.1016/j.tig.2013.04.003 · Cited by 115 · see citing works

Developments in RNA Splicing and Disease

Poulos, M. G., Batra, R., Charizanis, K., & Swanson, M. S. (2011) · Cold Spring Harbor Perspectives in Biology · doi:10.1101/cshperspect.a000778 · Cited by 98 · see citing works

Identification of a DNA Damage–Induced Alternative Splicing Pathway That Regulates p53 and Cellular Senescence Markers

Chen, J., Crutchley, J., Zhang, D., Owzar, K., & Kastan, M. B. (2017) · Cancer Discovery · doi:10.1158/2159-8290.cd-16-0908 · Cited by 93 · see citing works

Networking in a global world: establishing functional connections between neural splicing regulators and their target transcripts

Calarco, J. A., Zhen, M., & Blencowe, B. J. (2011) · RNA · doi:10.1261/rna.2603911 · Cited by 72 · see citing works

GWAS of multiple neuropathology endophenotypes identifies new risk loci and provides insights into the genetic risk of dementia

Shade, L. M. P., Katsumata, Y., Abner, E. L., Aung, K. Z., Claas, S. A., Qiao, Q., Heberle, B. A., Brandon, J. A., Page, M. L., Hohman, T. J., et al. (2024) · Nature Genetics · doi:10.1038/s41588-024-01939-9 · Cited by 72 · see citing works

FUS-regulated region- and cell-type-specific transcriptome is associated with cell selectivity in ALS/FTLD

Fujioka, Y., Ishigaki, S., Masuda, A., Iguchi, Y., Udagawa, T., Watanabe, H., Katsuno, M., Ohno, K., & Sobue, G. (2013) · Scientific Reports · doi:10.1038/srep02388 · Cited by 46 · see citing works

P3‐120: Mis‐splicing of Tau Exon 2 and Exon 10 in myotonic dystrophy brain would result from different mechanisms

Caillet‐Boudin, M., Dhaenens, C., Frandemiche, M., et al. (2011) · Alzheimer s & Dementia · doi:10.1016/j.jalz.2011.05.1561

Characterization of the mechanisms behind the alternative splicing of the mutually exclusive exons 18N and 18A in the sodium channel gene SCN8A and mutually exclusive exons 5N and 5A in the soldium channel gene SCN9A

Zubović, L. (2011) · Open Research Online (The Open University) · doi:10.21954/ou.ro.0000d62a

Repositioning of an alternative exon sequence of mouse IgM pre-mRNA activates splicing of the preceding intron.

Watakabe, A., Sakamoto, H., & Shimura, Y. (1991) · PubMed · Cited by 23 · see citing works

The importance of being divisible by three in alternative splicing

Magen, A. (2005) · Nucleic Acids Research · doi:10.1093/nar/gki858 · Cited by 65 · see citing works

Alternative splicing produces structural and functional changes in CUGBP2

Suzuki, H., Takeuchi, M., Sugiyama, A., et al. (2012) · BMC Biochemistry · doi:10.1186/1471-2091-13-6 · Cited by 18 · see citing works